@article{oai:repo.qst.go.jp:00080437,
 author = {Sakuraba, Shun and Iwakiri, Junichi and Hamada, Michiaki and Kameda, Tomoshi and Tsuji, Genichiro and Kimura, Yasuaki and Abe, Hiroshi and Asai, Kiyoshi and Sakuraba, Shun},
 issue = {9},
 journal = {Journal of the Computational and Theoretical Chemistry},
 month = {Sep},
 note = {Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases.},
 pages = {5925--5935},
 title = {Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters},
 volume = {16},
 year = {2020}
}